Tracing the origin and history of the HIV-2 epidemic

Abstract

In this study we date the introduction of HIV-2 into the human population and estimate the epidemic history of HIV-2 subtype A in Guinea-Bissau, the putative geographic origin of HIV-2. The evolutionary history of the simian immunodeficiency virus sooty mangabey͞HIV-2 lineage was reconstructed by using available database sequences with known sampling dates, and a timescale for this history was calculated by using maximum likelihood methods. The date of the most recent common ancestor of HIV-2 subtype A strains was estimated to be 1940 ؎ 16 and that of B strains was estimated to be 1945 ؎ 14. In addition we used coalescent theory to estimate the past population dynamics of HIV-2 subtype A in a rural population of Guinea-Bissau. Parametric and nonparametric estimates of the effective number of infections through time were obtained for an equal sample of gag, pol, and env sequences. Our estimates of the epidemic history of HIV-2 subtype A in Guinea-Bissau show a transition from constant size to rapid exponential growth around 1955-1970. Our analysis provides evidence for a zoonotic transfer of HIV-2 during the first half of the 20th century and an epidemic initiation in Guinea-Bissau that coincides with the independence war (1963)(1964)(1965)(1966)(1967)(1968)(1969)(1970)(1971)(1972)(1973)(1974), suggesting that war-related changes in sociocultural patterns had a major impact on the HIV-2 epidemic.T he AIDS epidemic is clearly recognized as a viral zoonosis (1-3). Phylogenetic analysis indicates that multiple interspecies transmissions from simian species have introduced two genetically distinct types of HIV into the human population: HIV-1, closely related to simian immunodeficiency virus (SIV) from chimpanzees (SIV CPZ ), and HIV-2, closely related to SIV from sooty mangabeys (SIV SM ). Whereas HIV-1 group M subtypes (A-D, F, H, J, and K) are spread globally, HIV-2 subtypes are mainly restricted to West Africa and can be categorized as epidemic subtypes (A and B) and nonepidemic subtypes (C-G) (4-7). Biological reasons have been invoked to explain the difference in global epidemiology between HIV-1 and HIV-2, such as lower HIV-2 viral loads that correlate with a lower transmissibility (8-10). However, attempts to compare the history of the epidemics at their respective geographic origins are still lacking.A useful strategy for investigating the epidemic history of HIV combines molecular clock analysis, to estimate the timescale of the epidemic, and coalescent theory, to infer the demographic history of the virus (11). Various molecular clock calculations have dated the most recent common ancestor (MRCA) of HIV-1 group M around 1930 Ϯ 15 (12-14). HIV-1 group M has subsequently spread globally, generating the pandemic observed today. Here, we investigate the epidemic history of HIV-2 to test previously suggested hypotheses of its origin. We provide the first estimated dates of cross-species transmissions of HIV-2. Our results indicate a transfer of HIV-2 subtypes A and B from sooty mangabeys to humans during the fi...

Tracing the history of hepatitis B virus genotype D in western Japan

“…Such a significant cluster is suitable for a coalescent analysis. The specific demographic model based on the neutral theory [Pybus et al, 2001Lemey et al, 2003], which has a constant size in the past and changes to exponential growth until the present, was applied for investigating the Japanese endemic of HBV/D in Ehime. Several historical factors in Japan have probably affected the spread of HBV/D, such as an increase of intravenous drug abuse in the 1940s during and after World War II, and the increase of blood transfusion procedures and the use of non-sterilized medical materials in the 1960s and 1970s.…”

“…This model assumes a continuous epidemic process in which the viral transmission parameters remain constant through time. Model fitting was evaluated by likelihood ratio tests of the parametric ML estimates [Lemey et al, 2003;Pybus et al, 2003]. Approximate 95% confidence intervals for the parameters were estimated using the likelihood ratio test statistics.…”

“…Time t was then transformed to year using the same rate, assuming the collecting time to be the present. Figure 3 shows the skyline plots and population growth for the HBV patients in Ehime, according to a specific demographic model in Genie v3.0 with three parameters, a piecewise expansion growth model, which was evaluated by likelihood ratio testing [Lemey et al, 2003;Pybus et al, 2003]. Based on this molecular evolution, it was estimated that the divergence time of the most recent common ancestor of HBV/D in Ehime was also estimated to be approximately 1,900.…”

Phylogénie des SIV et des VIH

“…Quant au VIH-1 du groupe N, il n'a été retrouvé que chez quelques personnes vivant au Cameroun [21]. Si le virus ancestral du VIH-1 M a bien été identifié au Cameroun, il n'en demeure pas moins que la plus grande diversité génétique du VIH-1 M en termes de nombre de sous-types et de diversité intra soustype a été observée dans la partie occidentale de la RDC suggérant que l'épicentre de l'épidémie du VIH-1 du groupe M est situé dans cette région d'Afrique [22,23] [30]. Bien que le mode exact de transmission des virus simiens (SIVcpz et SIVsmm) à l'homme ne soit pas connu, l'exposition à du sang ou à des sécrétions d'animaux infectés à l'occasion de la chasse ou de la préparation de la viande de brousse semble la cause la plus probable de contamination.…”

Méthodes alternatives pour l’étude de la diversité génétique rétrovirale simienne

“…L'essentiel des collections muséales est en effet constitué de spécimens capturés dans la nature. L'intérêt de ces spécimens est d'autant plus grand que les transmissions de VIH-1 et VIH-2 ont sûrement eu lieu dans la première moitié du siècle dernier [7,8], période au cours de laquelle les collections se sont considéra-blement enrichies. Mais cet intérêt potentiel ne fait bien sûr sens qu'à la condition que l'amplification d'ADN proviral à partir d'os ou de peau soit possible.…”